Bowtie2 alignment with file.txt

Question

[luzglongoria]

Hi there,

I am doing an alignment with bowtie2. I have paired-end files and I would like to include a .txt file for doing the alignment. By reading the manual I have found that I should use the command -12 and then the PATH for the tab-delimited .txt file. But then I get an error message:

My command:

 bowtie2 --threads 4 --local --no-unal -x /home/luz_garcia_longoria/workspace/reference_genomes/parasitereference.fasta -q -k 1 --al aligned_reads.fastq -12 /home/luz_garcia_longoria/workspace/samples.txt > aligned_host_parasite.sam

Error message:

Error: 1 mate files/sequences were specified with -1, but 0
mate files/sequences were specified with -2.  The same number of mate files/
sequences must be specified with -1 and -2.
Error: Encountered internal Bowtie 2 exception (#1)
Command: /var/bin/bowtie2-2.3.1/bowtie2-align-s --wrapper basic-0 --threads 4 --local -x 
/home/luz_garcia_longoria/workspace/reference_genomes/parasitereference.fasta -q -k 1 -12 --passthrough /home/luz_garcia_longoria/workspace/samples.txt 
(ERR): bowtie2-align exited with value 1`

I also show you how my .txt file looks like:

SP1     s21     /PATH/s21_1.fq    /PATH/s21_2.fq
SP1     s22     /PATH/s22_1.fq    /PATH/s22_2.fq
SP2     s31     /PATH/s31_1.fq    /PATH/s31_2.fq
SP2     s32     /PATH/s32_1.fq    /PATH/s32_2.fq

Is it something wrong with the .txt file?

[Bastien Hervé]

I never used this fonctionnality but it looks like you have to create 2 mate files (one for each mate), like this :

-1 /home/luz_garcia_longoria/workspace/samples_mate1.txt -2 /home/luz_garcia_longoria/workspace/samples_mate2.txt

Nevermind I don't think you can do that neither

Answer 1

[GenoMax]

-1 and -2 options are comma separate lists of file names. Not a separate txt file like you show.

-1 <m1>

Comma-separated list of files containing mate 1s (filename usually includes _1), e.g. -1 flyA_1.fq,flyB_1.fq. Sequences specified with this option must correspond file-for-file and read-for-read with those specified in <m2>. Reads may be a mix of different lengths. If - is specified, bowtie2 will read the mate 1s from the “standard in” or “stdin” filehandle.

-2 <m2>

Comma-separated list of files containing mate 2s (filename usually includes _2), e.g. -2 flyA_2.fq,flyB_2.fq. Sequences specified with this option must correspond file-for-file and read-for-read with those specified in <m1>. Reads may be a mix of different lengths. If - is specified, bowtie2 will read the mate 2s from the “standard in” or “stdin” filehandle.

[luzglongoria]

so then, there is no option in bowtie for include a text file with all the information about the samples?